Most store owners have preferences when it comes to using certain payment gateways. You might prefer most of your revenue going through a payment gateway that accepts credit cards, like Stripe, but still allow users to use PayPal. For situations like this, you can charge an extra fee on the order based on the payment gateway, to encourage users to use the cheaper option.
You should install and activate the Payment Gateway based Fees extension available on WooThemes.com.
In order to add a fee per gateway using Payment Gateway based Fees, go through the following steps:
During the checkout experience, you'll now see a fee when you select a payment gateway with a fee:
In this recipe, I have only covered the options you need to get started. There are a few more options you can tweak to get it working just the way you want. For a full list of options, see the documentation for this plugin at http://docs.woothemes.com/document/payment-gateway-based-fees/.